[yt-users] Problem dealing with FITS data in yt
tazkera haque
h.tazkera at gmail.com
Fri Sep 8 14:10:26 PDT 2017
Hi Nathan ,
I encountered an error after
$pip install -e .
RuntimeError: Building yt from source requires Cython 0.24 or newer but
Cython 0.23.4 is installed. Please update Cython using the appropriate
so i did
$ cdh
$ sudo pip install --upgrade Cython
$ Requirement already up-to-date: Cython in
/usr/local/lib/python2.7/dist-packages
Cleaning up...
$ cython --version
$ Cython version 0.23.4
so how do I upgrade to cython 0.24? DO I need to do that inside the yt
directory?
On Fri, Sep 8, 2017 at 3:36 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:
> Then you already have a directory named "yt". Delete it and make the
> clone, or clone to a new directory:
>
> $ git clone https://github.com/yt-project/yt ./yt-repo
>
> On Fri, Sep 8, 2017 at 2:35 PM, tazkera haque <h.tazkera at gmail.com> wrote:
>
>> OK Thanks. I $conda uninstall yt and then
>>
>> $ git clone https://github.com/yt-project/yt
>> fatal: destination path 'yt' already exists and is not an empty directory.
>>
>>
>>
>>
>> On Fri, Sep 8, 2017 at 3:28 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>> The fix is only available if you build yt from the git repository for
>>> now. We will do a release sometime in the next few weeks to make the fix
>>> generally available.
>>>
>>> For now, you can install yt from git following these steps:
>>>
>>> $ conda uninstall yt
>>> $ git clone https://github.com/yt-project/yt
>>> $ cd yt
>>> $ pip install -e .
>>>
>>> -Nathan
>>>
>>> On Fri, Sep 8, 2017 at 2:21 PM, tazkera haque <h.tazkera at gmail.com>
>>> wrote:
>>>
>>>> Hi Nathan,
>>>>
>>>> Thanks. I see the bug has been fixed according to the post, but I am
>>>> still getting the same error with that file. I updated yt to the latest
>>>> version and rebooted my laptop. Do I need to do anything else to get it
>>>> work out?
>>>>
>>>> Best
>>>> Tazkera
>>>>
>>>> On Thu, Sep 7, 2017 at 3:37 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>>>> wrote:
>>>>
>>>>> I've opened an issue, let's move discussion over there:
>>>>>
>>>>> https://github.com/yt-project/yt/issues/1552
>>>>>
>>>>> Tazkera, you can subscribe to notifications on the issue by clicking
>>>>> the subscribe button.
>>>>>
>>>>> On Thu, Sep 7, 2017 at 2:35 PM, John Zuhone <jzuhone at gmail.com> wrote:
>>>>>
>>>>>> Hi Tazkera,
>>>>>>
>>>>>> Thanks for uploading your file—it will make it far simpler to debug.
>>>>>> I’ll have a look at this and get back to you.
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> John
>>>>>>
>>>>>> On Sep 7, 2017, at 3:24 PM, tazkera haque <h.tazkera at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>> HI People,
>>>>>>
>>>>>> I am sorry to ask you a very novice question, but I am new to deal
>>>>>> with FITS data and I wanted to load it into yt to do some processing. I
>>>>>> uploaded my file here.
>>>>>>
>>>>>> First of all, I am trying to load my first FITS data in yt and it
>>>>>> returns me an error which I don't understand:
>>>>>>
>>>>>> *import yt*
>>>>>>
>>>>>>
>>>>>>
>>>>>> *ds = yt.load("signal_wfilt_sn.fits")ds.print_stats()*
>>>>>>
>>>>>>
>>>>>> *the error:*
>>>>>>
>>>>>> yt : [WARNING ] 2017-09-07 15:12:42,963 Cannot find time
>>>>>> yt : [INFO ] 2017-09-07 15:12:42,965 Detected these axes: RA---TAN DEC--TAN
>>>>>> yt : [WARNING ] 2017-09-07 15:12:42,979 No length conversion provided. Assuming 1 = 1 cm.
>>>>>> yt : [INFO ] 2017-09-07 15:12:42,996 Parameters: current_time = 0.0
>>>>>> yt : [INFO ] 2017-09-07 15:12:42,997 Parameters: domain_dimensions = [1629 1629 1]
>>>>>> yt : [INFO ] 2017-09-07 15:12:43,001 Parameters: domain_left_edge = [ 0.5 0.5 0.5]
>>>>>> yt : [INFO ] 2017-09-07 15:12:43,004 Parameters: domain_right_edge = [ 1.62950000e+03 1.62950000e+03 1.50000000e+00]
>>>>>> yt : [INFO ] 2017-09-07 15:12:43,006 Parameters: cosmological_simulation = 0.0
>>>>>>
>>>>>> ---------------------------------------------------------------------------IndexError Traceback (most recent call last)<ipython-input-38-71d5999c6b09> in <module>() 1 import yt 2 ds2 = yt.load("/home/trina/Documents/ASTRO_732/A-01/signal_wfilt_sn.fits")----> 3 ds2.print_stats()
>>>>>> /home/trina/anaconda2/lib/python2.7/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.pyc in root_only(*args, **kwargs) 318 def root_only(*args, **kwargs): 319 if not parallel_capable:--> 320 return func(*args, **kwargs) 321 comm = _get_comm(args) 322 rv = None
>>>>>> /home/trina/anaconda2/lib/python2.7/site-packages/yt/data_objects/static_output.pyc in print_stats(self) 455 @parallel_root_only 456 def print_stats(self):--> 457 self.index.print_stats() 458 459 @property
>>>>>> /home/trina/anaconda2/lib/python2.7/site-packages/yt/data_objects/static_output.pyc in index(self) 417 raise RuntimeError("You should not instantiate Dataset.") 418 self._instantiated_index = self._index_class(--> 419 self, dataset_type=self.dataset_type) 420 # Now we do things that we need an instantiated index for 421 # ...first off, we create our field_info now.
>>>>>> /home/trina/anaconda2/lib/python2.7/site-packages/yt/frontends/fits/data_structures.pyc in __init__(self, ds, dataset_type) 90 self._handle = ds._handle 91 self.float_type = np.float64---> 92 GridIndex.__init__(self,ds,dataset_type) 93 94 def _initialize_data_storage(self):
>>>>>> /home/trina/anaconda2/lib/python2.7/site-packages/yt/geometry/geometry_handler.pyc in __init__(self, ds, dataset_type) 56 # potentially quite expensive, and should be done with the indexing. 57 mylog.debug("Detecting fields.")---> 58 self._detect_output_fields() 59 60 def _initialize_state_variables(self):
>>>>>> /home/trina/anaconda2/lib/python2.7/site-packages/yt/frontends/fits/data_structures.pyc in _detect_output_fields(self) 171 continue 172 if self._ensure_same_dims(hdu):--> 173 units = self._determine_image_units(hdu.header, known_units) 174 try: 175 # Grab field name from btype
>>>>>> /home/trina/anaconda2/lib/python2.7/site-packages/yt/frontends/fits/data_structures.pyc in _determine_image_units(self, header, known_units) 116 n += 1 117 if n != len(units): field_units = "dimensionless"--> 118 if field_units[0] == "/": 119 field_units = "1%s" % field_units 120 return field_units
>>>>>> IndexError: string index out of range
>>>>>>
>>>>>> Can you Please suggest me how to load and work on this data?
>>>>>>
>>>>>> My goal is to create an image from the signal to noise data in the data file 'signal_wfilt_sn.fits' using only data
>>>>>> within 20 arcminutes of the center of the image. the pixel size is 3x3 arc second
>>>>>>
>>>>>> I had an initial code in mind which will create a sphere with a radius of 20 arcminute:
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> *import ytds = yt.load("signal_wfilt_sn.fits")ds.print_stats()sp = ds.sphere(ds.domain_center, (400, 'code_length'))*
>>>>>>
>>>>>> However, I first need to be able to load and explore the data. Your help and suggestion is greatly appreciated.
>>>>>>
>>>>>> Thanks a lot
>>>>>>
>>>>>>
>>>>>> Tazkera
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> <signal_wfilt_sn.fits>_______________________________________________
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>>>>>>
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